Designing primers with higher taxonomic distinguishability

Melita Jaric, Jonathan Segal, Eugenia Silva-Herzog, Lisa Schneper, Kalai Mathee, Giri Narasimhan

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Current methods of understanding microbiome composition and structure rely on accurately estimating the number species and their relative abundance. Most of these methods require an efficient PCR whose forward and reverse primers bind well to the same, large number of identifiable species, and produce amplicons that are unique. It is therefore not surprising that currently used universal primers designed many years ago are not as efficient and fail to bind to recently cataloged species. We propose an automated general method of designing PCR primer pairs that abide by primer design rules and since the method is automated, primers can be designed for targeted groups of microbial species or updated when a database is updated. In silico experiments and laboratory experiments confirm the efficacy of the newly designed primers for metagenomics applications.

Original languageEnglish (US)
Title of host publicationProceedings - 29th Southern Biomedical Engineering Conference, SBEC 2013
Pages157-158
Number of pages2
DOIs
StatePublished - Aug 5 2013
Event29th Southern Biomedical Engineering Conference, SBEC 2013 - Miami, FL, United States
Duration: May 3 2013May 5 2013

Publication series

NameProceedings - 29th Southern Biomedical Engineering Conference, SBEC 2013

Other

Other29th Southern Biomedical Engineering Conference, SBEC 2013
CountryUnited States
CityMiami, FL
Period5/3/135/5/13

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Experiments
Chemical analysis

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering

Cite this

Jaric, M., Segal, J., Silva-Herzog, E., Schneper, L., Mathee, K., & Narasimhan, G. (2013). Designing primers with higher taxonomic distinguishability. In Proceedings - 29th Southern Biomedical Engineering Conference, SBEC 2013 (pp. 157-158). [6525724] (Proceedings - 29th Southern Biomedical Engineering Conference, SBEC 2013). https://doi.org/10.1109/SBEC.2013.87
Jaric, Melita ; Segal, Jonathan ; Silva-Herzog, Eugenia ; Schneper, Lisa ; Mathee, Kalai ; Narasimhan, Giri. / Designing primers with higher taxonomic distinguishability. Proceedings - 29th Southern Biomedical Engineering Conference, SBEC 2013. 2013. pp. 157-158 (Proceedings - 29th Southern Biomedical Engineering Conference, SBEC 2013).
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Jaric, M, Segal, J, Silva-Herzog, E, Schneper, L, Mathee, K & Narasimhan, G 2013, Designing primers with higher taxonomic distinguishability. in Proceedings - 29th Southern Biomedical Engineering Conference, SBEC 2013., 6525724, Proceedings - 29th Southern Biomedical Engineering Conference, SBEC 2013, pp. 157-158, 29th Southern Biomedical Engineering Conference, SBEC 2013, Miami, FL, United States, 5/3/13. https://doi.org/10.1109/SBEC.2013.87

Designing primers with higher taxonomic distinguishability. / Jaric, Melita; Segal, Jonathan; Silva-Herzog, Eugenia; Schneper, Lisa; Mathee, Kalai; Narasimhan, Giri.

Proceedings - 29th Southern Biomedical Engineering Conference, SBEC 2013. 2013. p. 157-158 6525724 (Proceedings - 29th Southern Biomedical Engineering Conference, SBEC 2013).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Jaric M, Segal J, Silva-Herzog E, Schneper L, Mathee K, Narasimhan G. Designing primers with higher taxonomic distinguishability. In Proceedings - 29th Southern Biomedical Engineering Conference, SBEC 2013. 2013. p. 157-158. 6525724. (Proceedings - 29th Southern Biomedical Engineering Conference, SBEC 2013). https://doi.org/10.1109/SBEC.2013.87